cwl/imputation/rtg-vcfmerge.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.1
   6 class: CommandLineTool
   7 hints:
   8   DockerRequirement:
   9     dockerPull: vcfutil
  10   ResourceRequirement:
  11     ramMin: 5000
  12 inputs:
  13   sample: string
  14   vcf:
  15     type: File
  16     secondaryFiles: [.tbi]
  17   phasedvcf:
  18     type: File
  19     secondaryFiles: [.tbi]
  20   imputedvcf:
  21     type: File
  22     secondaryFiles: [.tbi]
  23 outputs:
  24   phasedimputedvcf:
  25     type: File
  26     outputBinding:
  27       glob: "*.vcf.gz"
  28     secondaryFiles: [.tbi]
  29 baseCommand: [rtg, vcfmerge]
  30 arguments:
  31   - "--force-merge-all"
  32   - $(inputs.phasedvcf)
  33   - $(inputs.vcf)
  34   - $(inputs.imputedvcf)
  35   - prefix: "-o"
  36     valueFrom: $(inputs.sample)_phased_imputed.vcf.gz